*Target (protein/gene name): S-adenosylmethionine Synthetase *NCBI Gene # or RefSeq#: metK945389 *Protein ID (NP or XP #) or Wolbachia#: NP_417417.1 *Organism (including strain): Burkholderia pseudomallei Etiologic Risk Group (see link below): Risk group 2 */Disease Information (sort of like the Intro to your Mini Research Write up): Burkholderia pseudomallei is a gram negative, rod-shaped bacterium that causes the disease melioidosis. It is found in soil and water in areas such as Thailand and northern Australia. Signs and symptoms include pain in the chest, bones and joints, and it also causes lung nodules and pneumonia. This bacteria also causes Glanders, with formation of nodular lesions in the lungs and ulceration of the mucous membranes in the upper respiratory tract. Link to TDR Targets page (if present): Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.) http://www.ncbi.nlm.nih.gov/gene/945389 http://www.uniprot.org/uniprot/P0A817
Essentiality of this protein: Involved in DNA methylation, and controls gene expression. Is it a monomer or multimer as biological unit? (make prediction athttp://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): dimer Complex of proteins?: Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): 0.5 in M. tuberculosis
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): -- link to Sigma (or other company) page for assay (see Sigma links below) -- -or link (or citation) to paper that contains assay information -- links to assay reagents (substrates) pages. --- List cost and quantity of substrate reagents, supplier, and catalog #
Structure (PDB or Homology model) -- PDB # or closest PDB entry if using homology model: 3IML (PDB) -- For Homology Model option: ---- Show pairwise alignment of your BLASTP search in NCBI against the PDB ---- Query Coverage: ---- Max % Identities: ---- % Positives ---- Chain used for homology:
Current Inhibitors: Expression Information (has it been expressed in bacterial cells): E. coli Purification Method: Image of protein (PyMol with features delineated and shown separately):
Crystal Structure Of S-Adenosylmethionine Synthetase From Burkholderia Pseudomallei
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
MANDYLFTSESVSEGHPDKVADQISDAILDAILAQDKYSRVAAETLCNTGLVVLAGEITT
TANIDYIQIARDTIKRIGYDNTDYGIDYRGCAVLVAYDKQSPDIAQGVDRAHDNNLDQGA
GDQGLMFGYACDETPELMPLPIHLSHRLVERQANLRRDGRLPWLRPDAKSQVTVRYVDGK
PHSIDTVVLSTQHAPEIDLPALREAVIEEVIKPTLPADLIKGDIKFLVNPTGRFVIGGPQ
GDCGLTGRKIIVDTYGGAAPHGGGAFSGKDPSKVDRSAAYAGRYVAKNIVAAGLASRALI
QVSYAIGVAEPTSVMVNTFGTGRVSDETITKLVREHFDLRPKGIIQMLDLLRPIYEKTAA
YGHFGREEPEFSWEAADKALALAEAAGVEPAVQVAX *length of your protein in Amino Acids: 396aa Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 42.7525kDa Molar Extinction coefficient of your protein at 280 nm wavelength: 33600 TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. *CDS Gene Sequence (paste as text only): ATGGCGAACGACTATCTGTTCACCTCTGAATCTGTTTCTGAAGGTCACCCGGACAAAGTT GCGGATCAAATCTCTGACGCGATTCTGGACGCAATCCTCGCGCAAGACAAATACTCTCGT GTTGCGGCGGAAACCCTGTGCAATACGGGTCTGGTTGTTCTCGCAGGTGAAATCACCACT ACCGCGAACATTGACTACATCCAAATTGCGCGTGACACCATCAAACGTATTGGTTACGAT AATACCGACTACGGTATCGACTACCGTGGTTGCGCGGTTCTCGTCGCGTACGACAAGCAA TCTCCGGACATCGCGCAGGGCGTTGACCGTGCGCATGACAATAATCTGGACCAGGGTGCG GGCGATCAGGGCCTGATGTTCGGTTATGCGTGCGACGAAACCCCAGAACTGATGCCGCTC CCGATCCACCTGTCTCACCGTCTGGTCGAACGTCAGGCGAACCTCCGCCGTGACGGTCGC CTGCCGTGGCTCCGTCCTGACGCAAAAAGCCAGGTTACCGTCCGTTACGTTGACGGCAAA CCGCATTCTATCGACACCGTTGTCCTGTCTACCCAGCACGCTCCGGAAATTGACCTGCCG GCTCTCCGTGAAGCGGTTATCGAAGAAGTTATCAAACCAACCCTCCCTGCCGACCTGATC AAAGGTGACATCAAATTCCTGGTGAATCCGACTGGCCGCTTCGTAATCGGTGGTCCGCAG GGTGACTGCGGTCTCACGGGTCGTAAAATCATTGTTGACACCTACGGTGGCGCAGCACCA CACGGTGGTGGTGCGTTCTCTGGTAAAGATCCGTCTAAAGTTGATCGTTCTGCGGCCTAC GCTGGTCGTTATGTAGCGAAAAACATCGTTGCAGCCGGTCTGGCGTCTCGTGCACTGATC CAGGTCTCTTACGCTATCGGCGTTGCCGAACCGACCTCTGTTATGGTTAATACCTTCGGT ACTGGTCGCGTTAGCGATGAAACCATTACCAAACTCGTTCGTGAACACTTCGACCTGCGC CCGAAGGGTATCATCCAGATGCTGGACCTGCTGCGTCCGATCTACGAAAAAACTGCTGCT TACGGTCACTTTGGTCGTGAAGAACCGGAATTCTCTTGGGAAGCTGCGGATAAAGCGCTC GCTCTGGCCGAGGCTGCGGGTGTTGAACCAGCGGTTCAGGTTGCGTAA *GC% Content for gene: *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): *GC% Content for gene (codon optimized): ATGGCGAACGACTATCTGTTCACCTCTGAATCTGTT GAGATTTGATCCGCAACTTTGTCCGGGTGACCTTCAGAAACAGATTCAGAGGTGAACAGA ACAAAGTTGCGGATCAAATCTCTGACGCGATTCTGGACGCAATCCTCGCGCAAGACAAAT CAGACCCGTATTGCACAGGGTTTCCGCCGCAACACGAGAGTATTTGTCTTGCGCGAGGAT CCTGTGCAATACGGGTCTGGTTGTTCTCGCAGGTGAAATCACCACTACCGCGAACATTGA AACCAATACGTTTGATGGTGTCACGCGCAATTTGGATGTAGTCAATGTTCGCGGTAGTGG GACACCATCAAACGTATTGGTTACGATAATACCGACTACGGTATCGACTACCGTGGTTGC CGATGTCCGGAGATTGCTTGTCGTACGCGACGAGAACCGCGCAACCACGGTAGTCGATAC AAGCAATCTCCGGACATCGCGCAGGGCGTTGACCGTGCGCATGACAATAATCTGGACCAG CACGCATAACCGAACATCAGGCCCTGATCGCCCGCACCCTGGTCCAGATTATTGTCATGC CTGATGTTCGGTTATGCGTGCGACGAAACCCCAGAACTGATGCCGCTCCCGATCCACCTG CGTCACGGCGGAGGTTCGCCTGACGTTCGACCAGACGGTGAGACAGGTGGATCGGGAGCG AACCTCCGCCGTGACGGTCGCCTGCCGTGGCTCCGTCCTGACGCAAAAAGCCAGGTTACC ACGGTGTCGATAGAATGCGGTTTGCCGTCAACGTAACGGACGGTAACCTGGCTTTTTGCG CGCATTCTATCGACACCGTTGTCCTGTCTACCCAGCACGCTCCGGAAATTGACCTGCCGG GGGTTGGTTTGATAACTTCTTCGATAACCGCTTCACGGAGAGCCGGCAGGTCAATTTCCG CGAAGAAGTTATCAAACCAACCCTCCCTGCCGACCTGATCAAAGGTGACATCAAATTCCT GGACCACCGATTACGAAGCGGCCAGTCGGATTCACCAGGAATTTGATGTCACCTTTGATC GCTTCGTAATCGGTGGTCCGCAGGGTGACTGCGGTCTCACGGGTCGTAAAATCATTGTTG CGCACCACCACCGTGTGGTGCTGCGCCACCGTAGGTGTCAACAATGATTTTACGACCCGT ACACGGTGGTGGTGCGTTCTCTGGTAAAGATCCGTCTAAAGTTGATCGTTCTGCGGCCTA AGACCGGCTGCAACGATGTTTTTCGCTACATAACGACCAGCGTAGGCCGCAGAACGATCA ATCGTTGCAGCCGGTCTGGCGTCTCGTGCACTGATCCAGGTCTCTTACGCTATCGGCGTT CCAGTACCGAAGGTATTAACCATAACAGAGGTCGGTTCGGCAACGCCGATAGCGTAAGAG TGGTTAATACCTTCGGTACTGGTCGCGTTAGCGATGAAACCATTACCAAACTCGTTCGTG GCATCTGGATGATACCCTTCGGGCGCAGGTCGAAGTGTTCACGAACGAGTTTGGTAATGG CGAAGGGTATCATCCAGATGCTGGACCTGCTGCGTCCGATCTACGAAAAAACTGCTGCTT CCAAGAGAATTCCGGTTCTTCACGACCAAAGTGACCGTAAGCAGCAGTTTTTTCGTAGAT TGAAGAACCGGAATTCTCTTGGGAAGCTGCGGATAAAGCGCTCGCTCTGGCCGAGGCTGC TTACGCAACCTGAACCGCTGGTTCAACACCCGCAGCCTCGGCCAGAG Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): DNA Works output Primer design results for 'tail' primers (this is just 2 sequences): Ordered and designed by Marissa Hansen Forward: 5' TAC TTC CAA TCC ATG GCG AAA CAC CTC TTC ACG 3' Reverse: 5' TAT CCA CCT TTA CTG TTA TTT GAG ACC TGC GGC ATC3' **
*NCBI Gene # or RefSeq#: metK 945389
*Protein ID (NP or XP #) or Wolbachia#: NP_417417.1
*Organism (including strain): Burkholderia pseudomallei
Etiologic Risk Group (see link below): Risk group 2
*/Disease Information (sort of like the Intro to your Mini Research Write up):
Burkholderia pseudomallei is a gram negative, rod-shaped bacterium that causes the disease melioidosis. It is found in soil and water in areas such as Thailand and northern Australia. Signs and symptoms include pain in the chest, bones and joints, and it also causes lung nodules and pneumonia. This bacteria also causes Glanders, with formation of nodular lesions in the lungs and ulceration of the mucous membranes in the upper respiratory tract.
Link to TDR Targets page (if present):
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)
http://www.ncbi.nlm.nih.gov/gene/945389
http://www.uniprot.org/uniprot/P0A817
Essentiality of this protein: Involved in DNA methylation, and controls gene expression.
Is it a monomer or multimer as biological unit? (make prediction at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): dimer
Complex of proteins?:
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): 0.5 in M. tuberculosis
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0053851
*EC#: 2.5.1.6
Link to BRENDA EC# page:
http://www.brenda-enzymes.info/enzyme.php?ecno=2.5.1.6&Suchword=&organism%5B%5D=Escherichia+coli&show_tm=0
-- ATP +
ATP + L-methionine + H2O = phosphate + diphosphate + S-adenosyl L - methionine
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-- link to Sigma (or other company) page for assay (see Sigma links below)
-- -or link (or citation) to paper that contains assay information
-- links to assay reagents (substrates) pages.
--- List cost and quantity of substrate reagents, supplier, and catalog #
Structure (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model: 3IML (PDB)
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage:
---- Max % Identities:
---- % Positives
---- Chain used for homology:
Current Inhibitors:
Expression Information (has it been expressed in bacterial cells): E. coli
Purification Method:
Image of protein (PyMol with features delineated and shown separately):
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
MANDYLFTSESVSEGHPDKVADQISDAILDAILAQDKYSRVAAETLCNTGLVVLAGEITT
TANIDYIQIARDTIKRIGYDNTDYGIDYRGCAVLVAYDKQSPDIAQGVDRAHDNNLDQGA
GDQGLMFGYACDETPELMPLPIHLSHRLVERQANLRRDGRLPWLRPDAKSQVTVRYVDGK
PHSIDTVVLSTQHAPEIDLPALREAVIEEVIKPTLPADLIKGDIKFLVNPTGRFVIGGPQ
GDCGLTGRKIIVDTYGGAAPHGGGAFSGKDPSKVDRSAAYAGRYVAKNIVAAGLASRALI
QVSYAIGVAEPTSVMVNTFGTGRVSDETITKLVREHFDLRPKGIIQMLDLLRPIYEKTAA
YGHFGREEPEFSWEAADKALALAEAAGVEPAVQVAX
*length of your protein in Amino Acids: 396aa
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 42.7525kDa
Molar Extinction coefficient of your protein at 280 nm wavelength: 33600
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
ATGGCGAACGACTATCTGTTCACCTCTGAATCTGTTTCTGAAGGTCACCCGGACAAAGTT
GCGGATCAAATCTCTGACGCGATTCTGGACGCAATCCTCGCGCAAGACAAATACTCTCGT
GTTGCGGCGGAAACCCTGTGCAATACGGGTCTGGTTGTTCTCGCAGGTGAAATCACCACT
ACCGCGAACATTGACTACATCCAAATTGCGCGTGACACCATCAAACGTATTGGTTACGAT
AATACCGACTACGGTATCGACTACCGTGGTTGCGCGGTTCTCGTCGCGTACGACAAGCAA
TCTCCGGACATCGCGCAGGGCGTTGACCGTGCGCATGACAATAATCTGGACCAGGGTGCG
GGCGATCAGGGCCTGATGTTCGGTTATGCGTGCGACGAAACCCCAGAACTGATGCCGCTC
CCGATCCACCTGTCTCACCGTCTGGTCGAACGTCAGGCGAACCTCCGCCGTGACGGTCGC
CTGCCGTGGCTCCGTCCTGACGCAAAAAGCCAGGTTACCGTCCGTTACGTTGACGGCAAA
CCGCATTCTATCGACACCGTTGTCCTGTCTACCCAGCACGCTCCGGAAATTGACCTGCCG
GCTCTCCGTGAAGCGGTTATCGAAGAAGTTATCAAACCAACCCTCCCTGCCGACCTGATC
AAAGGTGACATCAAATTCCTGGTGAATCCGACTGGCCGCTTCGTAATCGGTGGTCCGCAG GGTGACTGCGGTCTCACGGGTCGTAAAATCATTGTTGACACCTACGGTGGCGCAGCACCA
CACGGTGGTGGTGCGTTCTCTGGTAAAGATCCGTCTAAAGTTGATCGTTCTGCGGCCTAC
GCTGGTCGTTATGTAGCGAAAAACATCGTTGCAGCCGGTCTGGCGTCTCGTGCACTGATC
CAGGTCTCTTACGCTATCGGCGTTGCCGAACCGACCTCTGTTATGGTTAATACCTTCGGT
ACTGGTCGCGTTAGCGATGAAACCATTACCAAACTCGTTCGTGAACACTTCGACCTGCGC
CCGAAGGGTATCATCCAGATGCTGGACCTGCTGCGTCCGATCTACGAAAAAACTGCTGCT
TACGGTCACTTTGGTCGTGAAGAACCGGAATTCTCTTGGGAAGCTGCGGATAAAGCGCTC
GCTCTGGCCGAGGCTGCGGGTGTTGAACCAGCGGTTCAGGTTGCGTAA
*GC% Content for gene:
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
*GC% Content for gene (codon optimized):
ATGGCGAACGACTATCTGTTCACCTCTGAATCTGTT GAGATTTGATCCGCAACTTTGTCCGGGTGACCTTCAGAAACAGATTCAGAGGTGAACAGA ACAAAGTTGCGGATCAAATCTCTGACGCGATTCTGGACGCAATCCTCGCGCAAGACAAAT CAGACCCGTATTGCACAGGGTTTCCGCCGCAACACGAGAGTATTTGTCTTGCGCGAGGAT CCTGTGCAATACGGGTCTGGTTGTTCTCGCAGGTGAAATCACCACTACCGCGAACATTGA AACCAATACGTTTGATGGTGTCACGCGCAATTTGGATGTAGTCAATGTTCGCGGTAGTGG GACACCATCAAACGTATTGGTTACGATAATACCGACTACGGTATCGACTACCGTGGTTGC
CGATGTCCGGAGATTGCTTGTCGTACGCGACGAGAACCGCGCAACCACGGTAGTCGATAC AAGCAATCTCCGGACATCGCGCAGGGCGTTGACCGTGCGCATGACAATAATCTGGACCAG CACGCATAACCGAACATCAGGCCCTGATCGCCCGCACCCTGGTCCAGATTATTGTCATGC CTGATGTTCGGTTATGCGTGCGACGAAACCCCAGAACTGATGCCGCTCCCGATCCACCTG CGTCACGGCGGAGGTTCGCCTGACGTTCGACCAGACGGTGAGACAGGTGGATCGGGAGCG AACCTCCGCCGTGACGGTCGCCTGCCGTGGCTCCGTCCTGACGCAAAAAGCCAGGTTACC ACGGTGTCGATAGAATGCGGTTTGCCGTCAACGTAACGGACGGTAACCTGGCTTTTTGCG CGCATTCTATCGACACCGTTGTCCTGTCTACCCAGCACGCTCCGGAAATTGACCTGCCGG GGGTTGGTTTGATAACTTCTTCGATAACCGCTTCACGGAGAGCCGGCAGGTCAATTTCCG CGAAGAAGTTATCAAACCAACCCTCCCTGCCGACCTGATCAAAGGTGACATCAAATTCCT GGACCACCGATTACGAAGCGGCCAGTCGGATTCACCAGGAATTTGATGTCACCTTTGATC GCTTCGTAATCGGTGGTCCGCAGGGTGACTGCGGTCTCACGGGTCGTAAAATCATTGTTG CGCACCACCACCGTGTGGTGCTGCGCCACCGTAGGTGTCAACAATGATTTTACGACCCGT ACACGGTGGTGGTGCGTTCTCTGGTAAAGATCCGTCTAAAGTTGATCGTTCTGCGGCCTA AGACCGGCTGCAACGATGTTTTTCGCTACATAACGACCAGCGTAGGCCGCAGAACGATCA ATCGTTGCAGCCGGTCTGGCGTCTCGTGCACTGATCCAGGTCTCTTACGCTATCGGCGTT CCAGTACCGAAGGTATTAACCATAACAGAGGTCGGTTCGGCAACGCCGATAGCGTAAGAG TGGTTAATACCTTCGGTACTGGTCGCGTTAGCGATGAAACCATTACCAAACTCGTTCGTG GCATCTGGATGATACCCTTCGGGCGCAGGTCGAAGTGTTCACGAACGAGTTTGGTAATGG CGAAGGGTATCATCCAGATGCTGGACCTGCTGCGTCCGATCTACGAAAAAACTGCTGCTT CCAAGAGAATTCCGGTTCTTCACGACCAAAGTGACCGTAAGCAGCAGTTTTTTCGTAGAT TGAAGAACCGGAATTCTCTTGGGAAGCTGCGGATAAAGCGCTCGCTCTGGCCGAGGCTGC TTACGCAACCTGAACCGCTGGTTCAACACCCGCAGCCTCGGCCAGAG
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
DNA Works output
Primer design results for 'tail' primers (this is just 2 sequences): Ordered and designed by Marissa Hansen
Forward: 5' TAC TTC CAA TCC ATG GCG AAA CAC CTC TTC ACG 3'
Reverse: 5' TAT CCA CCT TTA CTG TTA TTT GAG ACC TGC GGC ATC3'
**